Cargando…
A critical assessment of gene catalogs for metagenomic analysis
MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiv...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479683/ https://www.ncbi.nlm.nih.gov/pubmed/33792639 http://dx.doi.org/10.1093/bioinformatics/btab216 |
_version_ | 1784576311040147456 |
---|---|
author | Commichaux, Seth Shah, Nidhi Ghurye, Jay Stoppel, Alexander Goodheart, Jessica A Luque, Guillermo G Cummings, Michael P Pop, Mihai |
author_facet | Commichaux, Seth Shah, Nidhi Ghurye, Jay Stoppel, Alexander Goodheart, Jessica A Luque, Guillermo G Cummings, Michael P Pop, Mihai |
author_sort | Commichaux, Seth |
collection | PubMed |
description | MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY AND IMPLEMENTATION: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8479683 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-84796832021-09-30 A critical assessment of gene catalogs for metagenomic analysis Commichaux, Seth Shah, Nidhi Ghurye, Jay Stoppel, Alexander Goodheart, Jessica A Luque, Guillermo G Cummings, Michael P Pop, Mihai Bioinformatics Original Papers MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY AND IMPLEMENTATION: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-04-01 /pmc/articles/PMC8479683/ /pubmed/33792639 http://dx.doi.org/10.1093/bioinformatics/btab216 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Commichaux, Seth Shah, Nidhi Ghurye, Jay Stoppel, Alexander Goodheart, Jessica A Luque, Guillermo G Cummings, Michael P Pop, Mihai A critical assessment of gene catalogs for metagenomic analysis |
title | A critical assessment of gene catalogs for metagenomic analysis |
title_full | A critical assessment of gene catalogs for metagenomic analysis |
title_fullStr | A critical assessment of gene catalogs for metagenomic analysis |
title_full_unstemmed | A critical assessment of gene catalogs for metagenomic analysis |
title_short | A critical assessment of gene catalogs for metagenomic analysis |
title_sort | critical assessment of gene catalogs for metagenomic analysis |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479683/ https://www.ncbi.nlm.nih.gov/pubmed/33792639 http://dx.doi.org/10.1093/bioinformatics/btab216 |
work_keys_str_mv | AT commichauxseth acriticalassessmentofgenecatalogsformetagenomicanalysis AT shahnidhi acriticalassessmentofgenecatalogsformetagenomicanalysis AT ghuryejay acriticalassessmentofgenecatalogsformetagenomicanalysis AT stoppelalexander acriticalassessmentofgenecatalogsformetagenomicanalysis AT goodheartjessicaa acriticalassessmentofgenecatalogsformetagenomicanalysis AT luqueguillermog acriticalassessmentofgenecatalogsformetagenomicanalysis AT cummingsmichaelp acriticalassessmentofgenecatalogsformetagenomicanalysis AT popmihai acriticalassessmentofgenecatalogsformetagenomicanalysis AT commichauxseth criticalassessmentofgenecatalogsformetagenomicanalysis AT shahnidhi criticalassessmentofgenecatalogsformetagenomicanalysis AT ghuryejay criticalassessmentofgenecatalogsformetagenomicanalysis AT stoppelalexander criticalassessmentofgenecatalogsformetagenomicanalysis AT goodheartjessicaa criticalassessmentofgenecatalogsformetagenomicanalysis AT luqueguillermog criticalassessmentofgenecatalogsformetagenomicanalysis AT cummingsmichaelp criticalassessmentofgenecatalogsformetagenomicanalysis AT popmihai criticalassessmentofgenecatalogsformetagenomicanalysis |